R E S E A R C H

Robert Kincaid is a Senior Research Scientist at Keysight Laboratories, the central research laboratory of Keysight Technologies.  Robert's main research interests are centered around visualization and user interface research to support interactive and visually-oriented data mining across combinations of widely disparate data. For in further details consult his CV/Resume.

From a computer science perspective these research interests group into roughly three categories:

1. Information Visualization and Visual Analytics - These are efforts to effectively visualize large multivariate datasets in ways that reveal insights in the data. Of course most of this data comes from Agilent life science instruments. Some examples include:

Big Data: This new direction for Kincaid's research is scaleable analytics (including visualization). Areas of current investigation include scalable computational techniques as well as large scale text mining to extract knowledge from large collections of scientific papers (such as the co-author network shown on the left). Much of this work is based on MapReduce technologies, particularly via Apache Spark. Stay tuned...

Agilent MassHunter IMS Software: This project leveraged visualization techniques created in previous research projects to provide critical  user interface design as well as novel visualization components for a new Agilent Mass Spectrometry platform that included Ion Mobility separation. This product was announced at the

Signal Lens: A Focus+Context approach for analyzing large time series of electronic signals. SignalLens enables a very compact visualization which supports ad hoc visual data mining of long electronic time series. A brief video demo was presented by Agilent CTO Darlene Solomon at the IEEE MTT-S International Microwave Symposium in2009. This work presented at the 2010 IEEE Information Visualization Conference and received an honorable mention for best paper.

RFLP Decoder: This software was developed to support authenticating fish species; a problem important to the food industry and critical to complying with new regulations to protect endangered fish species from being overfished. This is now part of an Agilent product (Agilent DNA Fish ID Solution) and was published in the Journal of Visual Experiments. So you can see a complete demo of the lab protocol as well as the software.

MassVis: This project supported a novel proteomics workflow developed by Kurt Dejgaard at McGill University. A cleverly designed scatter plot interface provides a highly interactive information browser for discovery of putative protein complexes. Pattern similarity matching is used to match ‘‘profiles’’ of similar proteins as a predictor of membership in a protein complex. Both supervised, interactive methods are provided as well as completely unsupervised complex prediction. This work was presented at the 2009 IEEE Symposium on Visual Analytics Science and Technology. The MassVis concept has been awarded US Patent 7,930,108.

Line Graph Explorer

Line Graph Explorer: A scalable Focus+Context visualization designed specifically for large collections of line graphs. This work was done with the help of Heidi Lam at the University of British Columbia. Presented at AVI 2006, Venice Italy. You can also view a video demo (~100Mb!)

LGE was also featured on Information Aesthetics.

LGE is covered by two US Patents ( 7,825,929 and 7,750,908).

VistaChrom

VistaChrom: A visual environment for analyzing array-based comparative genomic hybridization data (aCGH). This was transferred as part of a new commercial aCGH platform and is now part of Agilent Genomic Workbench. See the recent publication in “Information Visualization” for details. Published in Information Visualization. [preprint]

VistaClara

VistaClara: An exploratory heat map style visualization of gene expression data that combines additional meta-data to assist in finding meaningful patterns and biological insight. Published in SAC 2004 Proceedings.

2. Human Computer Interaction - This is a new effort to explore how emerging user interface methods might influence the 21st century laboratory. Expect to see more of this in the future:

HCI of BioDesign for Synthetic Biology: This area is from a multi-year collaboration with Orit Shaer and her students at Wellesley College. This work includes several different approaches to using touch-enabled user interfaces as well as tangible objects to assist in designing assemblies of synthetic biology parts. Much of this work was in conjunction with the iGEM competition.

tactileguides.png
Tactile Guides for Touch Screens: This paper describes work-inprogress to investigate the use of simple transparent overlays that provide tactile guides for touch-based graphical control widgets. By augmenting the touch surface with a simple low-cost overlay, we aim to restore many of the tactile properties and benefits of standard physical controls. We have fabricated an initial proof-of-concept overlay and demonstration system and have performed a preliminary evaluation that suggests overlay guides may be beneficial. Published at HCI'12.

3. Computational Data Analysis - This is primarily concerned with low-level analysis of data from microarrays, liquid chromatography, mass spectrometry, or more recently electropherograms from the Agilent 2100 Bioanalyzer. Here is an example from Mass Spectrometry:

hdl subfractions
Deconvolution of HDL Subfractions: Agilent has developed an assay for measuring HDL subfractions from human serum using the Agilent Bioanalyzer microfluidic platform. This required a novel and fully automatic algorithm to fit Gaussian peak shapes to the expected fractions. This enabled deconvoluting the overlapping peaks and permitted measurements of the HDL components. This algorithm was used to measure data from real clinical samples as published in Clinical Chemistry and Laboratory Medicine (see Muller et al. 2007 below).
mass profiler

Mass Hunter/ Mass Profiler: A visual environment for analyzing proteomic and metabolomic biomarkers using Mass Spectrometry. This software was announced and demonstrated at ASMS 2005 and released in late 2005. I contributed the plotting graphics and user interface improvements.


Publications

Colin Swindells, Melanie Tory, Robert Kincaid, Guy Evans, Understanding and supporting histopathology slide sorting, Behaviour & Information Technology, 2016

C. Grote, E. Segreto, J. Okerlund, R. Kincaid, O. Shaer, Eugenie: Multi-Touch and Tangible Interaction for Bio-Design, Conference on Tangible, Embedded and Embodied Interaction (TEI’15).

C. Grote, E. Segreto, J. Okerlund, R. Kincaid, O. Shaer, Eugenie: Gestural and Tangible Interaction with Active Tokens for Bio-Design, Extended Abstract, ACM UIST 2014.

Orit Shaer, Consuelo Valdes, Sirui Liu, Kara Lu, Casey Grote, Veronica Lin, Linda Ding, Nicole Francisco, Kimberly Chang, Wendy Xu, Nahum Seifelassie, Robert Kincaid, Designing Reality-Based Interfaces for Experiential Bio-Design, Personal and Ubiquitous Computing (Special Edition on Educational Interfaces, Software, and Technology) 2014, 18: p. 1515-1532.

Melanie Tory, Robert Kincaid, Comparing Physical, Overlay, and Touch Screen Parameter Controls, ACM Interactive Tabletops and Surfaces 2013 Conference (ITS), 2013.

Orit Shaer, Consuelo Valdes, Sirui Liu, Kara Lu, Traci Haddock, Swapnil Bhatia, Douglas Densmore, Robert Kincaid, MoClo Planner: Interactive Visualization for Modular Cloning Bio-Design, Accepted IEEE Symposium on Biological Data Visualization (BioVis), 2013.

Wendy Xu, Kimberly Chang, Nicole Francisco, Consuelo Valdes, Robert Kincaid, and Orit Shaer, From Wet Lab Bench to Tangible Virtual Experiment: SynFlo. ACM International Conference on Tangible, Embedded and Embodied Interaction (TEI’13).

Kimberly Chang, Wendy Xu, Nicole Francisco, Consuelo Valdes, Robert Kincaid, and Orit Shaer, SynFlo: an interactive installation introducing synthetic biology concepts, ACM international conference on Interactive tabletops and surfaces (ITS '12) 303-306. (pdf)

Robert Kincaid, Tactile Guides for Touch Screen Controls (BCS HCI 2012) 339-344 (pdf)

Ankit Singh, Alex Endert, Lauren Bradel, Christopher Andrews, Chris North, Robert Kincaid,Using Large Displays for Live Visual History of Cyber-security Analytic Process (VizSec 2011) (pdf)

Steffen Mueller, Harini Ravi, Natalia Novoradovskaya, Robert Kincaid and Yang-Lee Chee, Enhanced fish species identification by PCR-RFLP using the 2100 Bioanalyzer system, International Food Research Journal 18, 3 (2011) 1154-1158 (pdf)

Robert Kincaid, SignalLens: Focus+Context Applied to Electronic Time Series, IEEE Transactions on Visualization and Computer Graphics (InfoVis ‘10), 2010, 16, 6 900-907 (pdf)

Formosa R, Ravi H, Happe S, Huffman D, Novoradovskaya N, Kincaid R, Garrett S (2010). DNA-based Fish Species Identification Protocol.Journal of Visualized Experiments. 38. http://www.jove.com/index/details.stp?id=1871, doi: 10.3791/1871 (link)

R. Kincaid, K. Dejgaard, MassVis: Visual Analysis of Protein Complexes Using Mass Spectrometry, IEEE Symposium on Visual Analytics Science and Technology (VAST ‘09), Atlantic City NJ, October 11-12 2009. (pdf)

A. Barsky, T. Munzner, J. Gardy, R. Kincaid, Cerebral: Visualizing Multiple Experimental Conditions on a Graph with Biological Context, IEEE Transactions on Visualization and Computer Graphics (InfoVis ‘08), 2008, 14, 6 1253-1260. (pdf)

R. Kincaid, A. Kuchinsky, M. Creech, VistaClara: an expression browser plug-in for Cytoscape, Bioinformatics 24, 18 (2008) 2112. (pdf)

Mueller, O.; Chang, E.; Deng, D.; Franz, T.; Jing, D.; Kincaid, R.; Konigshofer, Y.; Kratzmeier, M.; McNulty, M.; Qian, H.; Schneider, J.; Schulte, H.; Seedorf, U.; Tian, X.; Cleve, M. V.; Yang, D.; Assmann, G., PROCAM Study: risk prediction for myocardial infarction using microfluidic high density lipoprotein (HDL) sub-fractionation is independent of HDL-cholesterol. Clinical Chemistry and Laboratory Medicine 2008, 46(4) 490-498. (pdf)

Lam, H.; Munzner, T.; Kincaid, R., Overview use in multiple visual information resolution interfaces. IEEE Transactions on Visualization and Computer Graphics (IEEE InfoVis ‘07), 2007, 13(6) 1278-1285. (pdf)

R. Kincaid, H. Lam, Line Graph Explorer: Scalable Display of Line Graphs Using Focus+Context, Proc. of the Workshop on Advanced Visual Interfaces (AVI'06), ACM Press, Venice, Italy 2006. (pdf)
D. X. Deng, A. Tsalenko, A. Vailaya, A. Ben-Dor, R. Kundu, I. Estay, R. Tabibiazar, R. Kincaid, Z. Yakhini, L. Bruhn, T. Quertermous, Differences in vascular bed disease susceptibility reflect differences in gene expression response to atherogenic stimuli, Circulation Research 98, 2 (2006) 200.

R. Kincaid, A. Ben-Dor, Z. Yakhini, Exploratory visualization of array-based comparative genomic hybridization, Information Visualization 4, 3 (2005) 176. [preprint]

J. Y. King, R. Ferrara, R. Tabibiazar, J. M. Spin, M. M. Chen, A. Kuchinsky, A. Vailaya, R. Kincaid, A. Tsalenko, D. X.-F. Deng, A. Connolly, P. Zhang, E. Yang, C. Watt, Z. Yakhini, A. Ben-Dor, A. Adler, L. Bruhn, P. Tsao, T. Quertermous, E. A. Ashley, Pathway analysis of coronary atherosclerosis, Physiol. Genomics (2005) 00101.2005.

A. Vailaya, P. Bluvas, R. Kincaid, A. Kuchinsky, M. Creech, A. Adler, An architecture for biological information extraction and representation, Bioinformatics 21, 4 (2005) 430.

M. T. Barrett, A. Scheffer, A. Ben-Dor, N. Sampas, D. Lipson, R. Kincaid, P. Tsang, B. Curry, K. Baird, P. S. Meltzer, Z. Yakhini, L. Bruhn, S. Laderman, Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA, Proceedings of the National Academy of Sciences of the United States of America 101, 51 (2004) 17765.

R. Kincaid, VistaClara: an interactive visualization for exploratory analysis of DNA microarrays, Proceedings of the 2004 ACM symposium on Applied computing (SACBIO 2004), ACM Press, Nicosia, Cyprus 2004.

A. Vailaya, P. Bluvas, R. Kincaid, A. Kuchinsky, M. Creech, A. Adler, An architecture for biological information extraction and representation, Proceedings of the 2004 ACM symposium on Applied computing (SACBIO 2004), ACM Press, Nicosia, Cyprus 2004.


Issued US Patents

8,340,389 Cellular- or Sub-Cellular-Based Visualization Information Using Virtual Stains
8,131,471 Systems and methods for focus plus context viewing of dense, ordered line graphs
8,131,471 Methods and system for simultaneous visualization and manipulation of multiple data types
7,930,108 Exploratory visualization of protein complexes by molecular weight
7,894,998 Method for identifying suitable nucleic acid probe sequences for use in nucleic acid arrays
7,879,541 Apparatus and methods of detecting features on a microarray
7,825,929 Systems, tools and methods for focus and context viewing of large collections of graphs
7,750,908 Focus plus context viewing and manipulation of large collections of graphs
7,588,889 Chemical arrays and methods of using the same
7,519,605 Systems, methods and computer readable media for performing a domain-specific metasearch, and visualizing search results therefrom
7,344,831 Methods for controlling cross-hybridization in analysis of nucleic acid sequences
7,224,362 Systems and methods for providing visualization and network diagrams
7,155,453 Biotechnology information naming system
6,950,756 Rearrangement of microarray scan images to form virtual arrays
6,920,448 Domain specific knowledge-based metasearch system and methods of using
6,461,816 Methods for controlling cross-hybridization in analysis of nucleic acid sequences
6,251,588 Method for evaluating oligonucleotide probe sequences